Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2003;4(5):R33.
doi: 10.1186/gb-2003-4-5-r33. Epub 2003 Apr 25.

A novel exploratory method for visual recombination detection

Korbinian Strimmer  1 , Kristoffer Forslund, Barbara Holland, Vincent Moulton
Affiliations
Comparative Study

A novel exploratory method for visual recombination detection

Korbinian Strimmer et al. Genome Biol. 2003.

Abstract

A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. The method is based on two novel diagrams - the highway plot and the occupancy plot - that graphically portray phylogenetic inhomogeneity along an alignment, and can be viewed as a synthesis of two widely used but unrelated methods: bootscanning and quartet-mapping. To illustrate the method, simulated data and HIV-1 and influenza A datasets are investigated.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Highway and occupancy plots for simulated data with no recombination.
Figure 2
Figure 2
Highway and occupancy plots for simulated data with recombination and balanced trees.
Figure 3
Figure 3
Highway and occupancy plots for simulated data with recombination and unbalanced trees.
Figure 4
Figure 4
Highway and occupancy plots for an HIV-1 gag region alignment containing the recombinant sequence 93BR029. The red vertical lines indicate the two putative breakpoints.
Figure 5
Figure 5
Highway and occupancy plots for the 1918 influenza virus dataset. The window size varies from 400 to 800 bp.
Figure 6
Figure 6
Bootscan plots. (a) HIV-1 data; (b) 1918 influenza virus data.
Figure 7
Figure 7
The quartet-mapping triangle. (a) Barycentric coordinate system; (b) polar representation. In both (a) and (b), C denotes the centroid (1/3, 1/3, 1/3) and P some general point (s1, s2, s3).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Schierup MH, Hein J. Recombination and the molecular clock. Mol Biol Evol. 2000;17:1578–1579. - PubMed
    1. Schierup MH, Hein J. Consequences of recombination on traditional phylogenetic analysis. Genetics. 2000;156:879–891. - PMC - PubMed
    1. Posada D, Crandall KA. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol. 2001;16:37–45. - PubMed
    1. Posada D, Crandall KA. The effect of recombination on the accuracy of phylogeny reconstruction. J Mol Evol. 2002;54:396–402. - PubMed
    1. Wiuf C, Christensen T, Hein J. A simulation study of the reliability of recombination detection methods. Mol Biol Evol. 2001;18:1929–1939. - PubMed

Publication types

LinkOut - more resources